Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi18g1250 Blo01g01332 Blo12g01105 Bda01g00698 Bda03g00034 Bpe02g00609 Bpe04g00023 Bma04g00032 Bma01g02116 Cmo04g02551 Cmo15g00619 Cma01g00988 . Car01g00880 . . Cpe06g00896 Cpe13g00670 . . . . . . . Cla08g00677 Cam08g1107 Cec08g0692 Cco08g0801 Clacu08g0813 . Cre08g0617 Cone4ag1510 Cone7ag1441 Cone17ag0794 Cone20ag0391 . . . Cme03g00380 Blo17g00217 Blo18g00216 . Bda13g01525 Bpe02g01605 Bpe14g00336 Bma01g00865 Bma02g00275 . Cmo01g01025 . . . Car04g02348 Car09g00994 Cpe01g02108 . Bhi09g01500 . . . . . . Cla09g00924 Cam09g0977 Cec09g0982 Cco09g0988 . . Cre09g0945 Lsi08g00535 . Chy03g00542 .
Vvi18g1251 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1252 Blo01g01333 . . . . . . . . Cmo12g00289 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1253 . . . . . . . . Cmo04g02552 Cmo15g00618 . . . . Sed11g1337 . Cpe13g00671 Bhi04g01799 Tan11g1166 Cmetu03g0441 . . . . Cla08g00678 Cam08g1108 Cec08g0694 Cco08g0802 Clacu08g0814 . Cre08g0618 . . Cone17ag0793 Cone20ag0389 . . . Cme03g00377 Blo17g00216 . . Bda13g01524 . Bpe14g00337 . Bma02g00274 . . . . . Car04g02349 Car15g00561 Cpe01g02109 . . . . . . . . . . . . . . . Lsi08g00536 . Chy03g00541 .
Vvi18g1254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1255 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1256 . . . . . . . . Cmo04g02557 Cmo15g00611 . . . . . . Cpe13g00675 Bhi04g01791 . . . . . Lcy10g1341 Cla08g00702 . . . . . . . . Cone17ag0791 Cone20ag0386 . . . Cme03g00342 . Blo18g00215 . Bda13g01522 Bpe02g01606 . Bma01g00863 Bma02g00273 . . . . . Car05g00693 Car15g00559 Cpe01g02111 . . . . . . . . . . . . . . . Lsi08g00545 . Chy03g00525 .
Vvi18g1257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1259 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34123933 34137419 + Bda002734.1 Bda01g00698 698
3 486484 492672 + Bda015967.1 Bda03g00034 34
13 38266301 38280590 + Bda000370.1 Bda13g01522 1522
13 38290998 38293435 - Bda000372.1 Bda13g01524 1524
13 38305052 38308168 - Bda000373.1 Bda13g01525 1525
4 43533671 43545598 + XM_039028645.1 Bhi04g01791 1791
4 44373816 44413262 + XM_039029047.1 Bhi04g01799 1799
9 39109171 39119018 + XM_039042230.1 Bhi09g01500 1500
1 50868512 50875934 + BLOR01332 Blo01g01332 1332
1 50876513 50877472 + BLOR01333 Blo01g01333 1333
12 28741846 28746844 - BLOR05124 Blo12g01105 1105
17 2226223 2228677 - BLOR16037 Blo17g00216 216
17 2230136 2239834 - BLOR16038 Blo17g00217 217
18 2094843 2112455 + BLOR08703 Blo18g00215 215
18 2122330 2142763 - BLOR08704 Blo18g00216 216
1 8108313 8119741 + Bma001084.1 Bma01g00863 863
1 8127306 8132206 - Bma001086.1 Bma01g00865 865
1 77370540 77372291 + Bma002948.2 Bma01g02116 2116
2 3146587 3157587 + Bma030870 Bma02g00273 273
2 3185376 3186573 - Bma014725.1 Bma02g00274 274
2 3190142 3193226 - Bma014726.1 Bma02g00275 275
4 355715 361704 + Bma018484.1 Bma04g00032 32
2 3963709 3980307 - Bpe008449.1 Bpe02g00609 609
2 18929340 18935291 + Bpe009451.1 Bpe02g01605 1605
2 18939425 18951271 - Bpe009452.1 Bpe02g01606 1606
4 222995 226253 + Bpe014749.1 Bpe04g00023 23
14 3247589 3252302 + Bpe006989.1 Bpe14g00336 336
14 3252990 3255406 + Bpe006990.1 Bpe14g00337 337
8 17453704 17462036 + CaPI482276_08g011070.1 Cam08g1107 1107
8 17468171 17474713 + CaPI482276_08g011080.1 Cam08g1108 1108
9 10103637 10110087 - CaPI482276_09g009770.1 Cam09g0977 977
1 8064384 8072722 - Carg25043-RA Car01g00880 880
4 18865849 18871265 + Carg15782-RA Car04g02348 2348
4 18872895 18877750 + Carg15783-RA Car04g02349 2349
5 4686215 4694121 - Carg19822-RA Car05g00693 693
9 6453846 6462374 - Carg27266-RA Car09g00994 994
15 3078254 3088487 + Carg01596-RA Car15g00559 559
15 3114687 3118368 - Carg01594-RA Car15g00561 561
8 19866657 19874879 + CcPI632755_08g008010.1 Cco08g0801 801
8 19879304 19888261 + CcPI632755_08g008020.1 Cco08g0802 802
9 9376439 9384383 - CcPI632755_09g009880.1 Cco09g0988 988
8 18672590 18680924 + CePI673135_08g006920.1 Cec08g0692 692
8 18694871 18702115 + CePI673135_08g006940.1 Cec08g0694 694
9 9391252 9401777 - CePI673135_09g009820.1 Cec09g0982 982
3 7286151 7299778 + Chy3G055050.1 Chy03g00525 525
3 7600969 7608707 - Chy3G055210.1 Chy03g00541 541
3 7619366 7627552 - Chy3G055220.1 Chy03g00542 542
8 18189910 18201333 + ClG42_08g0081300.10 Clacu08g0813 813
8 18210246 18218001 + ClG42_08g0081400.10 Clacu08g0814 814
8 19059591 19068956 + ClCG08G006620.1 Cla08g00677 677
8 19078840 19086197 + ClCG08G006630.1 Cla08g00678 678
8 19267285 19280659 - ClCG08G006880.2 Cla08g00702 702
9 9632854 9640073 - ClCG09G009900.2 Cla09g00924 924
1 7090568 7099794 - CmaCh01G009880.1 Cma01g00988 988
3 4558702 4576633 - MELO3C008367.2.1 Cme03g00342 342
3 5245015 5253732 - MELO3C008389.2.1 Cme03g00377 377
3 5277130 5286312 - MELO3C008391.2.1 Cme03g00380 380
3 9887060 9896167 - PI0010359.1 Cmetu03g0441 441
1 8025658 8035352 - CmoCh01G010250.1 Cmo01g01025 1025
4 18693764 18703284 + CmoCh04G025510.1 Cmo04g02551 2551
4 18704308 18708595 + CmoCh04G025520.1 Cmo04g02552 2552
4 18735020 18748470 - CmoCh04G025570.1 Cmo04g02557 2557
12 1832935 1835382 - CmoCh12G002890.1 Cmo12g00289 289
15 2962529 2972719 + CmoCh15G006110.1 Cmo15g00611 611
15 3002195 3005998 - CmoCh15G006180.1 Cmo15g00618 618
15 3006392 3015893 - CmoCh15G006190.1 Cmo15g00619 619
4 11730241 11737291 - Conep04aG0156200.1 Cone4ag1510 1510
7 10201294 10207722 + Conep07aG0148300.1 Cone7ag1441 1441
17 6136205 6156763 + Conep17aG0080900.1 Cone17ag0791 791
17 6200695 6203417 - Conep17aG0081100.1 Cone17ag0793 793
17 6217331 6224598 - Conep17aG0081200.1 Cone17ag0794 794
20 1812146 1822981 + Conep20aG0040000.1 Cone20ag0386 386
20 1843412 1846684 - Conep20aG0040300.1 Cone20ag0389 389
20 1862657 1870072 - Conep20aG0040500.1 Cone20ag0391 391
1 17822255 17829306 + Cp4.1LG01g21080.1 Cpe01g02108 2108
1 17830187 17835131 + Cp4.1LG01g21110.1 Cpe01g02109 2109
1 17859216 17873622 - Cp4.1LG01g21170.1 Cpe01g02111 2111
6 6052283 6061313 - Cp4.1LG06g07590.1 Cpe06g00896 896
13 6308036 6317628 + Cp4.1LG13g04160.1 Cpe13g00670 670
13 6317916 6321771 + Cp4.1LG13g04190.1 Cpe13g00671 671
13 6349189 6359100 - Cp4.1LG13g04120.1 Cpe13g00675 675
8 19107697 19116036 + CrPI670011_08g006170.1 Cre08g0617 617
8 19121135 19129166 + CrPI670011_08g006180.1 Cre08g0618 618
9 9598185 9606206 - CrPI670011_09g009450.1 Cre09g0945 945
10 36413953 36429509 - Maker00008698 Lcy10g1341 1341
8 13316285 13326380 + Lsi08G005350.1 Lsi08g00535 535
8 13329603 13335050 + Lsi08G005360.1 Lsi08g00536 536
8 13577550 13590978 - Lsi08G005450.1 Lsi08g00545 545
11 29122280 29131445 + Sed0002807.1 Sed11g1337 1337
11 9620025 9627698 - Tan0016698.1 Tan11g1166 1166
18 14160238 14172215 - Vvi18g1250 Vvi18g1250 1250
18 14204583 14205216 - Vvi18g1251 Vvi18g1251 1251
18 14207945 14210222 + Vvi18g1252 Vvi18g1252 1252
18 14210515 14227768 + Vvi18g1253 Vvi18g1253 1253
18 14276149 14276380 + Vvi18g1254 Vvi18g1254 1254
18 14293746 14294436 + Vvi18g1255 Vvi18g1255 1255
18 14296311 14329573 - Vvi18g1256 Vvi18g1256 1256
18 14365660 14379400 - Vvi18g1257 Vvi18g1257 1257
18 14379716 14382149 + Vvi18g1258 Vvi18g1258 1258
18 14382174 14384416 + Vvi18g1259 Vvi18g1259 1259
       

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